This seems like a bug to me. If I obsolete a core ship, for instance colony or constructor, it does not appear as buildable when I begin a new game. Obsolete or deleted core ships should reappear fresh if a new game is started!
For that matter, player designs should NOT carry on to new games. Maybe I want to begin a game with a different approach to my designer ships, and all those weird and not very efficient designs from my last game keep popping up. I mean, at first I thought I could play and experiment freely with designing ships, obsoleting them, etc. Now I see it is dangerous, as any changes I make will stay in the game forever!
The fun is lost, now if I want to design a ship it's homework, like, I better get it right the first time. And NO-NO making core ships obsolete! As the game progresses the build list gets full of ships I no longer need, I have to scroll down and down to find what I want. Making ships obsolete was much more straightforward in GC I, and it could be very easily undone.
Incidentally, I have suffered CTD's when saving or deleting ships (core or player). When they start happening, they keep on happening (i.e. I can no longer save/obsolete w/o suffering a CTD) needing a reinstall.